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This base, first seen in "Chuck Versus the Intersect", is the first of the Intersect bases in the series, and was where the government had decided to keep the original Intersect until it was destroyed. Fulcrum wanted to have control of the Intersect and so hired spy Bryce Larkin to steal the computer files for them.

On Chuck's birthday, Bryce broke into this base, downloaded the computer files to a remote device and then destroyed the original computer with high explosives. He then made his escape from the base using parkour and fighting skills he managed to get onto the roof and then made his way down to the ground floor by jumping down to different levels of the building. When he reached the ground floor, and it looked life he was home free, he was confronted by John Casey who shot him dead but not before he was able to send the Intersect computer files to Chuck.

Base #2 was seen a few times in the series, when Beckman was talking about how far along the Government, the CIA and the NSA, we to completing the Second Intersect which was housed within this room. This base's Intersect room looked like the previous room, all white with the Intersect control computer in the middle.

When the new Intersect was ready Langston Graham and a few other agents prepared to use the Intersect. It should be-noted that Graham was the only one wearing sun glasses, the only way to block the Intersect out of your brain, at the time meaning that the plan was for the other agents to become human Intersects like Chuck is. However all didn't go to plan as Fulcrum had replaced The Cipher, a device that acts as the brains for the Intersect, with a sabotage device which promptly blew up the New Intersect along with Graham, the agents and the room.

Base #3 like the other government Intersect rooms seen in the series is a white room woes walls are made up entirely of screens which, when the Intersect is activated, are used to project the Intersect files to be views by the people in the room.

In "Chuck Versus the Ring" Bryce escapes from the Ring agents gun fight by locking himself in this room but is unable to upload the Intersect as he has been shot. Chuck drops down from the ceiling, mirroring Bryce's entry into the Intersect room in "Chuck Versus the Intersect" and takes the Intersect Overload Cartridge handed to him by Bryce, ready to destroy the Intersect 2.0 before it can end up in the hands of The Ring. Chuck reconsiders, knowing that they need the Intersect to fight the ring and uploads the Intersect, destroying the computer after the upload is complete. The Ring burst into the room, with a captured Sarah and Casey causing Chuck to upload Kung Fu skills which he uses to fight off the ring agents

Whilst not a government Intersect building, it should be noted that Ring Intersect was housed in an Intersect room, though it did differ from the designs of the others mentioned above. The Ring Intersect, housed in a Ring facility.